Fibroblast growth patterns for diagnosis of alzheimer&#39;s disease

ABSTRACT

Methods of diagnosing Alzheimer&#39;s disease are provided. At least five methods of diagnostic measurements are presented: Method 1: Integrated score; Method 2: Average aggregate area per number of aggregates; Method 3: Cell migration analysis; Method 4: Fractal analysis; Method 5: Lacunarity Analysis. In certain embodiments, a sample of a subject&#39;s skin provides a network of fibroblasts that is imaged and a fractal dimension of the image is calculated. The fractal dimension can be compared to an aged-matched control (non-Alzheimer&#39;s) database to determine if the subject has Alzheimer&#39;s disease. The network of fibroblasts may be cultured in a matrix, for example in a protein mixture.

The instant application is a continuation of U.S. Ser. No. 14/176,233,filed on Feb. 10, 2014, which is a divisional of U.S. Ser. No.12/896,862, filed on Oct. 2, 2010, now U.S. Pat. No. 8,658,134, issuedon Feb. 25, 2014, which claims the benefit of priority to U.S.Provisional Application No. 61/248,368, filed Oct. 2, 2009, and U.S.Provisional Application No. 61/344,045, filed May 13, 2010, and U.S.Provisional Application No. 61/362,518, filed Jul. 8, 2010, and U.S.Provisional Application No. 61/365,545, filed Jul. 19, 2010, thedisclosures of which are hereby incorporated herein in their entireties.

FIELD OF THE INVENTION

The present invention relates to methods to diagnose Alzheimer's diseaseusing fibroblast growth patterns as a biomarker.

BACKGROUND OF THE INVENTION

Alzheimer's disease (AD) is a neurodegenerative disorder characterizedby the progressive decline of memory and cognitive functions. It isestimated that over five million Americans are living with thisprogressive and fatal disease. Alzheimer's destroys brain cells, causingmemory loss and problems with thinking and behavior that decreasequality of life. AD has no known cure, but treatments for symptoms canimprove the quality of life of the millions of people, and theirfamilies, suffering from AD. An early diagnosis of AD gives the patienttime to make choices that maximize quality of life, reduces anxietyabout unknown problems, gives more time to plan for the future, andprovides a better chance of benefiting from treatment.

There exists a need for highly sensitive and highly specific tests todiagnose Alzheimer's Disease. The present inventors have identified, forthe first time, unique Alzheimer's Disease-specific biomarkers usefulfor the diagnosis of Alzheimer's Disease in a highly sensitive andhighly specific manner compared to previously known diagnostic tests.Specifically, the inventors have identified fibroblast growth patternsas biomarkers for the diagnosis of Alzheimer's Disease. Thus, the uniqueAlzheimer's Disease-specific biomarkers disclosed herein serve as thebasis for diagnostic methods having a high degree of sensitivity andspecificity for the detection and diagnosis of Alzheimer's Disease. Theunique Alzheimer's Disease-specific biomarkers of the present inventionmay also be useful as a model of brain networks and for screeningmethods to identify compounds which may be used as therapeutic agents inthe treatment and prevention of Alzheimer's Disease.

SUMMARY OF THE INVENTION

The instant invention, in certain preferred embodiments, is directed tomethods of diagnosing Alzheimer's Disease using assays directed to fiveseparate methodologies, referred to herein as (1) the integrated scoremethods; (2) the average aggregate area per number of aggregatesmethods; (3) the cell migration analysis methods; (4) the fractalanalysis methods; and (5) the lacunarity analysis methods.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's Disease in a human subject comprising the stepsof (a) obtaining one or more cells from a human subject; (b) culturingsaid one or more cells for a time period; (c) determining the averagearea of cell aggregates and dividing said average area by the number ofaggregates to obtain the area per number of aggregates; (d) comparingthe determination of step (c) with the area per number of aggregatesdetermined using non-Alzheimer's Disease cells; and (e) diagnosing thepresence or absence of Alzheimer's Disease based on the comparison instep (d).

The method is positive for Alzheimer's Disease if the area per number ofaggregates determined in step (c) is greater than the area per number ofaggregates determined in step (d). In certain preferred embodiments, thedifference is statistically significant.

In preferred embodiments, the diagnosis is confirmed using one or moreadditional diagnostic methods. The method one or more additionaldiagnostic methods are selected from the group consisting of methodscomprising determining an integrated score, methods comprisingcalculating area per number of aggregates, methods comprising cellmigration analysis, methods comprising fractal analysis and methodscomprising lacunarity analysis.

In preferred embodiments, the methods disclosed herein use cells thatare fibroblasts although other cells such as blood cells or neural cellsmay be used.

In certain embodiments, the known non-Alzheimer's Disease cells are ACcells.

In certain embodiments, the cells are cultured in a protein mixture. Theprotein mixture may comprise an extracellular matrix preparationcomprising laminin, collagen, heparin sulfate proteoglycans,entactin/nidogen, and/or combinations thereof. The protein mixture mayfurther comprise growth factor. The extracellular matrix protein may beextracted from a tumor. In certain embodiments, the tumor is the EHSmouse sarcoma.

In certain embodiments, the invention is directed to methods comprising(a) obtaining one or more cells from a human subject; (b) culturing saidone or more cells for a time period; (c) obtaining an image of saidcells at the conclusion of said time period; (d) determining a fractaldimension associated with a network of cells on said image; (e)comparing the determination of step (d) with an independently determinedfractal dimension associated with known non-Alzheimer's disease cells.

In certain embodiments, if the fractal dimension calculated in step (d)is statistically significantly lower than the fractal dimensionassociated with known non-Alzheimer's Disease cells, the comparison isindicative of Alzheimer's Disease.

In preferred embodiments, the AD is confirmed using one or moreadditional diagnostic methods. The method one or more additionaldiagnostic methods are selected from the group consisting of methodscomprising determining an integrated score, methods comprisingcalculating area per number of aggregates, methods comprising cellmigration analysis, methods comprising fractal analysis and methodscomprising lacunarity analysis.

In certain embodiments, the fractal dimension is calculated using a boxcounting procedure. In certain embodiments, the box counting procedurecomprises an edge detection procedure.

In certain embodiments, the subject is aged-matched with a controlsubject providing known non-Alzheimer's disease cells. In certainembodiments, the cell culture period is about 24 hours or about 36 hoursor about 48 hours.

In certain embodiments, the cells are cultured in a protein mixture. Theprotein mixture may comprise an extracellular matrix preparationcomprising laminin, collagen, heparin sulfate proteoglycans,entactin/nidogen, and/or combinations thereof. The protein mixture mayfurther comprise growth factor. The extracellular matrix protein may beextracted from a tumor. In certain embodiments, the tumor is the EHSmouse sarcoma.

In certain embodiments, the invention is directed to methods comprising:(a) determining a fractal dimension of an image of a network offibroblasts from a human subject, (b) determining a fractal dimension ofan image of a network of fibroblasts from kno\.vn non-Alzheimer'sdisease cells; (c) comparing the determinations of steps (a) and (b).

In certain embodiments, if the fractal dimension determined in step (a)is statistically significantly lower than the fractal dimensiondetermined in step (b), the diagnosis is indicative of Alzheimer'sDisease.

In certain embodiments, said subject is aged-matched with a controlsubject providing said known non-Alzheimer's Disease cells.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's disease in a human subject, comprising: (a)calculating a fractal dimension of an image of a network of fibroblastsfrom said subject; (b) comparing the calculation of step (a) with anindependently determined fractal dimension associated with knownnon-Alzheimer's disease cells; wherein if the fractal dimensioncalculated in step (a) is statistically significantly lower than thefractal dimension associated with known non-Alzheimer's disease cells,the diagnosis is positive for Alzheimer's Disease in said subject.

In certain embodiments, said subject is aged-matched with a controlsubject providing said known non-Alzheimer's disease cells.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's disease in a human subject, the methodcomprising: (a) using a surgical blade to obtain a sample of saidsubject's peripheral skin fibroblasts; (b) using an incubator toincubate said sample for a time period; (c) using an imager to take animage of said sample at the conclusion of said time period; (d) using acomputer to calculate a fractal dimension associated with a network offibroblasts on said image; (e) comparing the calculation of step (d)with an independently determined fractal dimension associated with knownnon-Alzheimer's disease cells, wherein if the fractal dimensioncalculated in step (d) is statistically significantly lower than thefractal dimension associated with known non-Alzheimer's disease cells,the diagnosis is positive for Alzheimer's Disease in said subject.

In certain embodiments, the cells are cultured in a protein mixture. Theprotein mixture may comprise an extracellular matrix preparationcomprising laminin, collagen, heparin sulfate proteoglycans,entactin/nidogen, and/or combinations thereof. The protein mixture mayfurther comprise growth factor. The extracellular matrix protein may beextracted from a tumor. In certain embodiments, the rumor is the EHSmouse sarcoma.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's Disease in a human subject, the methodscomprising: (a) using a surgical blade to obtain a sample of saidsubject's peripheral skin fibroblasts; (b) using an incubator toincubate said sample for a time period; (c) using an imager to take animage of said sample at the conclusion of said time period; (d) using acomputer to calculate a fractal dimension associated with a network offibroblasts on said image; (e) using a computer to input the fractaldimension of step (d) into a database having fractal dimension datagenerated from non-Alzheimer's disease cells obtained from controlsubjects of various ages; (f) using a computer to diagnose said subjectby comparing the calculated fractal dimension of step (d) with the dataof said database.

In certain embodiments, the sample is incubated in a gelatinous proteinmixture.

In certain embodiments, the cells are cultured or incubated in agelatinous protein mixture. The protein mixture may comprise anextracellular matrix preparation comprising laminin, collagen, heparinsulfate proteoglycans, entactin/nidogen, and/or combinations thereof.The protein mixture may further comprise growth factor. Theextracellular matrix protein may be extracted from a tumor. In certainembodiments, the tumor is the EHS mouse sarcoma.

In certain embodiments, the invention is directed to a computer readablemedium having a database of fractal dimension data generated fromnon-Alzheimer's disease cells obtained from control subjects of variousages, said medium containing instructions to: (a) calculate a fractaldimension of an image; (b) compare said fractal dimension with saiddatabase of fractal dimension data; and (c) output a diagnosis based onthe comparison of step (b).

In certain embodiments, the invention is directed to methods comprising:(a) culturing a skin cell from a human subject for a time period; (b)measuring cell morphology characteristics associated with a network offibroblasts of said cell; (c) performing a calculation related to saidcell morphology characteristics; and (d) comparing the calculation ofstep (c) with an independently determined parameter associated withknown non-Alzheimer's disease cells.

In certain embodiments, the cell morphology characteristics are selectedfrom the group consisting of: number of fibroblast clumps (oraggregates), size of fibroblast clumps (or aggregates), growth offibroblast clumps (or aggregates), and combinations thereof.

In certain embodiments, the cell morphology characteristics are thepresence or absence of big clumps (or aggregates), the presence orabsence of cells attached to the clumps (or aggregates), the presence orabsence of big clumps (or aggregates) growing, the number of clumps (oraggregates), the presence or absence of remnant edges from a previouslyformed network of said clumps (or aggregates), the number of cellsmigrating, the presence or absence of cells being near percolation.

In certain embodiments, the calculation of step (c) comprises assigninga discrete value for each of said cell morphology characteristics andsumming said values.

In certain embodiments, the summation is used to diagnose AD or theabsence of AD.

In certain embodiments, the cells are cultured in a protein mixture. Theprotein mixture may comprise an extracellular matrix preparationcomprising laminin, collagen, heparin sulfate proteoglycans,entactin/nidogen, and/or combinations thereof. The protein mixture mayfurther comprise growth factor. The extracellular matrix protein may beextracted from a tumor. In certain embodiments, the tumor is the EHSmouse sarcoma.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's Disease in a subject comprising the steps of: (a)obtaining one or more cells from said subject and growing said one ormore cells in a tissue culture medium; (b) measuring the fractaldimension of said one or more cells over a time period; (c) plottingsaid fractal dimension as a function of time to obtain a fractaldimension curve: (d) comparing said fractal dimension curve to fractaldimension curves obtained from non-Alzheimer's Disease cells andnon-Alzheimer's Disease Dementia (non-ADD) cells; and (e) diagnosing thepresence or absence of Alzheimer's Disease in said subject.

In certain embodiments, the diagnosis is positive for Alzheimer'sDisease in said subject if said fractal dimension curve measured from acell or cells obtained from said subject is statistically significantlydifferent from said fractal dimension curves obtained from saidnon-Alzheimer's Disease cells and said non-ADD cells.

In certain embodiments, said cell or cells obtained from said subject isa fibroblast cell.

In preferred embodiments, the diagnosis is confirmed using one or moreadditional diagnostic methods. The method one or more additionaldiagnostic methods are selected from the group consisting of methodscomprising determining an integrated score, methods comprisingcalculating area per number of aggregates, methods comprising cellmigration analysis, methods comprising fractal analysis and methodscomprising lacunarity analysis.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's Disease in a subject comprising the steps of (a)obtaining one or more cells from said subject and growing said one ormore cells in a tissue culture medium; (b) determining an integratedscore based on one or more characteristics of said cultured cells; (c)comparing said integrated score to an integrated score determined fornon-Alzheimer's Disease cells; (d) diagnosing the presence or absence ofAlzheimer's Disease in said subject.

In certain embodiments, said characteristics used to calculate saidintegrated score are selected from the group consisting of aggregatesize, attachment of cells to aggregates, evidence of aggregate growth,number of aggregates, edges within networks, evidence of cell migrationand closeness to percolation limit (or cell density).

In preferred embodiments, the diagnosis is confirmed using one or moreadditional diagnostic methods. The method one or more additionaldiagnostic methods are selected from the group consisting of methodscomprising determining an integrated score, methods comprisingcalculating area per number of aggregates, methods comprising cellmigration analysis, methods comprising fractal analysis and methodscomprising lacunarity analysis.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's Disease in a subject comprising the steps of (a)obtaining one or more cells from said subject and growing said one ormore cells in a tissue culture medium; (b) determining the number ofmigrating cells; (c) comparing the number of migrating cells to thenumber of migrating cells for non-Alzheimer's Disease cells; (d)diagnosing the presence or absence of Alzheimer's Disease in saidsubject.

In certain embodiments, the diagnosis is positive for AD if the numberof migrating cells obtained from said subject is statisticallysignificantly smaller than the number of migrating non-Alzheimer'sDisease cells.

In certain embodiments, said cells are fibroblasts.

In preferred embodiments, the diagnosis is confirmed using one or moreadditional diagnostic methods. The method one or more additionaldiagnostic methods are selected from the group consisting of methodscomprising determining an integrated score, methods comprisingcalculating area per number of aggregates, methods comprising cellmigration analysis, methods comprising fractal analysis and methodscomprising lacunarity analysis.

In certain embodiments, the invention is directed to methods ofdiagnosing Alzheimer's Disease in a subject comprising the steps of (a)obtaining one or more cells from said subject and growing said one ormore cells in a tissue culture medium; (b) determining the lacunarity ofsaid cells; (c) comparing the lacunarity of said cells to the lacunarityof non-Alzheimer's Disease cells; (d) diagnosing the presence or absenceof Alzheimer's Disease in said subject.

In certain embodiments, the diagnosis is positive for AD if thelacunarity of the cells taken from said subject is statisticallysignificantly higher than the lacunarity of the non-Alzheimer's Diseasecells.

In preferred embodiments, the diagnosis is confirmed using one or moreadditional diagnostic methods. The method one or more additionaldiagnostic methods are selected from the group consisting of methodscomprising determining an integrated score, methods comprisingcalculating area per number of aggregates, methods comprising cellmigration analysis, methods comprising fractal analysis and methodscomprising lacunarity analysis.

In certain embodiments, said cells are fibroblasts.

In certain embodiments, the invention is directed to methods ofscreening fora lead compound useful for the development of one or moredrug candidates for the treatment or prevention of Alzheimer's diseasecomprising the steps of (a) growing one or more AD cells in a cellculture medium; (b) contacting said AD cells with a compound; (c)determining whether one or more characteristics of said AD cells isaltered to resemble the characteristics of non-Alzheimer's Disease cellsthat have not been contacted with said compound.

In certain embodiments said cells are fibroblasts.

In certain embodiments, said characteristic is fractal dimension or anintegrated score or an average aggregate area per number of aggregates,or cell migration, or lacunarity.

In certain embodiments, the invention is directed to methods ofdetermining Alzheimer's Disease duration in a subject comprising (a)obtaining one or more cells from said subject; (b) measuring cellmigration characteristics or average area per number of aggregates forknown AD cell lines; (c) preparing standard curves using the dataobtained in step (b); measuring migration characteristics or averagearea per number of aggregates for the cells obtained in step (a) and (d)determining AD disease duration in said subject.

In certain embodiments, said cells are fibroblasts.

In certain embodiments, subjects identified as having AD for 10, 9, 8,7, 6, 5, 4, 3, 2, or 1 years or less are identified as having increasedresponsiveness to treatment of AD.

In certain embodiments, the invention is directed to methods ofdistinguishing between the presence of Alzheimer's Disease (AD) andnon-Alzheimer's Disease Dementia (non-ADD) in a subject comprising: (a)obtaining one or more cells from a subject (b) measuring the fractaldimension of said one or more cells over a time period; (c) plottingsaid fractal dimension as a function of time to obtain a fractaldimension curve; (d) comparing said fractal dimension curve to fractaldimension curves obtained from known non-Alzheimer's Disease cells,known non-Alzheimer's Disease Dementia (non-ADD) cells and known ADcells; and (e) distinguishing between AD and non-ADD in said subject.

In certain embodiments, said cells are fibroblasts.

In certain embodiments, the invention is directed to methods ofdistinguishing between the presence of Alzheimer's Disease andnon-Alzheimer's Disease Dementia in a subject comprising: (a) obtainingone or more cells from a subject (b) obtaining one or more cells fromsaid subject and growing said one or more cells in a tissue culturemedium; (c) determining the number of migrating cells; (d) comparing thenumber of migrating cells to the number of migrating cells for knownnon-Alzheimer's Disease cells, known AD cells and known non-ADD cells;(e) distinguishing between AD and non-ADD in said subject.

In certain embodiments, said cells are fibroblasts.

In one embodiment, the invention provides a method of diagnosingAlzheimer's disease in a human subject, the method comprising: (a)calculating a fractal dimension of an image of a network of fibroblastsfrom said subject; (b) comparing the calculations of step (a) with anindependently determined fractal dimension associated with knownnon-Alzheimer's disease cells; wherein if the fractal dimensioncalculated in step (a) is statistically significantly lower than thefractal dimension associated with known non-Alzheimer's disease cells,the diagnosis is positive, and the diagnosis is negative otherwise; and(c) diagnosing.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Initial Preparation of Fibroblasts

FIG. 2: Integrated Score Protocol

FIG. 3: Fractal Analysis Protocol

FIG. 4: Integrated Score Method. Total scores representing the sum ofeight characteristics for skin cell fibroblasts (AC=age matchedcontrols; AD=Alzheimer's Disease: Non-ADD=Non-Alzheimer's such asParkinson's disease (PD) and Huntington's disease (HD) dementia at 48hours after plating.

FIGS. 5A and 5B: Examples of aggregates for Alzheimer's diseasefibroblasts (FIG. 5A) and normal controls (FIG. 5B). The area wasmeasured in μm² by fitting an ellipse across the aggregates and theaggregates were counted manually on the 10× images. Ellipses were fittedacross each aggregate so that the edges of aggregates are inside theellipse. The same procedure was used uniformly across all the images.

FIG. 6: Fibroblasts at 48 hours. The average area per number ofaggregates for 31 cell lines: age matched controls (N_(AC)=10),Alzheimer's disease (N_(AD)=12), and Non-Alzheimer's dementia(N_(Non-ADD)=9) such as Parkinson's disease (PD) and Huntington'sdisease (HD). The error bars represent the standard error of the mean.

FIG. 7: Repeatability of the results. The average area per number ofaggregates for four repeated cell lines. Experiments were at least onemonth apart for the same cell lines. Initial number of cells was within10%.

FIGS. SA and SB: Examples of freely migrating cells marked with reddots. Left picture (FIG. 8A) Alzheimer's disease (AD) and right picture(FIG. 8B) non-Alzheimer's dementia (Non-ADD; Huntington's disease)fibroblasts at 48 hours after plating.

FIG. 9: Migration rate versus number of migrating cells. Greensquares-Alzheimer's disease (N_(AD)=10), blue triangles-Non-Alzheimer'sdementia (N_(Non-ADD)=7), and red circles-age matched controls(N_(AC)=9). Blue lines are separating thresholds.

FIG. 10: Migration rate times the number of migrating cells. Greensquares—Alzheimer's disease (N_(AD)=10), blue triangles-Non-Alzheimer'sdementia (N_(Non-ADD)=7), and red circles-age matched controls(N_(AC)=9).

FIGS. 11A and 11B: Fractal analysis. FIG. 11A: Examples of fractalcurves and linear it of the recovery region. FIG. 11B: Population datashowing the slope versus intercept for fractal curves (N=31; N_(AC)=10;N_(AD)=12; N_(Non-ADD)=9).

FIGS. 12A and 12B: Lacunarity analysis. FIG. 12A: Examples oflacunarityl curves. FIG. 12B: Population data showing the averagelacunarity (N=8; N_(AC)=1; N_(AD)=4; N_(Non-ADD)=3).

FIG. 13: Proportionality relation between matrigel thickness and volumein 12 well plates. When the matrigel volume is in the range 400 to 800μl the thickness of the matrigel layer is in the range of 1.04 to 2.08mm.

FIGS. 14A and 14B: Sensitivity of fractal dimension, and lacunarity, onthe initial volume of matrigel. Fractal dimension (FIG. 14A), andlacunarity (FIG. 14B) have a qualitatively different trend for smallvolumes of matrigel 400 μl (red) and 500 μl (green) when compared withlarger volumes of matrigel 600 μl (blue), 700 μl (pink), and 800 μl(turquoise). For large volumes(>600 μl) the more matrigel is added thelarger the effect on fractal dimension (FIG. 14A), and lacunarity (FIG.14B). For reference, in all of the previous experiments we used 700 μlof matrigel.

FIGS. 15A and 15B: Sensitivity of AD aggregates at 48 hours on theinitial volume of matrigel. FIG. 15A: Area per number of aggregates at48 h and 79 h versus the initial volume of matrigel. FIG. 15B: Rate ofchange for area/number as a function of initial volume of matrigel. Thegraphs illustrate (1) the importance of using 700 μl of Matrigel wherethe curves show a peak and the effect is maximum. (2) The increase ofthe Alzheimer's aggregates in size and reduction in number in this timewindow 40-80 h. This is illustrated in panel A by showing the aggregatearea per number at two different time points 48 h and 79 h. The greencurve is above the red curve indicating a growth in area and/orreduction in number. Experimentally both are observed. Panel B shows arate of change in this measure Area/# between 48 h and 79 h. In otherwords, take the curves from panel A, subtract them and divide by thetime interval. The AD fibroblasts cells are unable to migrate away fromthe aggregates after 40 h. Therefore, the aggregates grow bigger for ADcells in this time window. For the control cases, AC, this is notobserved and cells are able to migrate away from the aggregates.

FIG. 16: Depicts age matched control (AC) fibroblasts networks after 24hours of incubation.

FIG. 17: Depicts Alzheimer's Disease (AD) patient fibroblasts networksafter 24 hours of incubation.

FIG. 18: Depicts the fractal dimensions of AC and AD subjects versustime.

FIG. 19: Depicts the fractal dimension of AD versus AC networks after 24hours of incubation.

FIGS. 20A and 20B: FIG. 20A: AD fibroblast cell lines. Graph showing alinear increase of the average aggregate area per number of aggregateswith disease duration. In other words, a direct correlation existsbetween disease duration and the (average aggregate area)/(number ofaggregates). The number next to each square is the number of cell linestested. FIG. 20B: AD fibroblast cell lines. Linear correlation betweendisease duration and number of migrating cells. The number next to eachsquare is the number of cell lines tested. Using these correlations, itis possible to identify patients that are in the early, middle or latestages of Alzheimer's Disease. Patients in the earlier stages of thedisease have an increased responsiveness to treatment. Knowledge of howlong a patient has had Alzheimer's Disease helps guide the therapeuticgoals and strategies employed in a treatment regime on apatient-by-patient basis.

DETAILED DESCRIPTION

Abbreviations: AC: age matched controls; AD: Alzheimer's Disease; AvC:Average number of cells; DC: density of cells; DMEM: Dulbecco's ModifiedEagle Medium; EtOH: Ethanol; FBS: Fetal Bovine Serum; Non-ADD: nonAlzheimer's dementias; RIM: Room Temperature.

As used herein, “lacunarity” refers to a measure of how a fractal fillsspace. It is used to further classify fractals and textures which, whilethey may share the same fractal dimension, appear very visuallydifferent. Dense fractals have a low lacunarity. As the coarseness ofthe fractal increases, so does the lacunarity; intuitively from lacunameaning “gap” ( . . . more gaps=higher lacunarity). Lacunarity istypically represented by the symbol L.

${L(r)} = \frac{{\sum_{m = 1}^{r^{2}}{m^{2}{P\left( {m,r} \right)}}} - \left( {\sum_{m = 1}^{r^{2}}{{mP}\left( {m,r} \right)}} \right)^{2}}{\left( {\sum_{m = 1}^{r^{2}}{{mP}\left( {m,r} \right)}} \right)^{2}}$

The present invention in certain embodiments, is related to methods todiagnose Alzheimer's disease (AD) using peripheral skin fibroblasts. Invarious embodiments of the invention, quantitative, qualitative, and/orsemi-quantitative aspects of the fibroblasts are used to determine thepresence or absence of AD.

In one embodiment, the method involves the quantification of thecomplexity of the human skin fibroblast networks with fractal dimensionsmeasurements. In another embodiment, the method involves calculating atotal score based on the sum of characteristics of skin cellfibroblasts. In another embodiment, the method involves calculating thearea per number of clumps of skin cell fibroblasts. The methods allowfor early screening of AD patients from non-AD dementia, and fromage-matched control (AC) cases.

A method to diagnose Alzheimer's disease (AD) using peripheral skinfibroblasts is described. This method quantifies the complexity of humanskin fibroblasts patterns of growth with measures of network formation,aggregation, communication, dynamic mobility on a specialized substrate(Matrigel), and fibroblast aggregates morphology.

Matrigel matrix is extracted from mouse sarcoma, rich in extracellularmatrix (ECM) proteins. It consists of laminin, followed by collagen TV,heparan sulfate proteoglycans, and entactin 1. At 37° C., matrigelpolymerizes to produce biologically active matrix material resemblingthe mammalian cellular basement membrane. BD Matrigel Matrix GrowthFactor Reduced (GFR) is found to be particularly well suited forapplications requiring a more highly defined basement membranepreparation of the gel substrate.

Five methods of diagnostic measurements are presented:

1. Method 1: Integrated score

2. Method 2: Average aggregate area per number of aggregates

3. Method 3: Cell migration analysis

4. Method 4 Fractal analysis

5. Method 5: Lacunarity Analysis

Additional measures of fibroblasts growth patterns may be developed todiagnostically distinguish between Alzheimer's disease (AD),non-Alzheimer's dementia (non-ADD) and age matched controls (AC) cellstaken from biopsy. Diagnostic efficacy may be improved by addingextracellular matrix modifying agents.

Method 1—Integrated Score

In this study skin fibroblasts within 1 to 2 hours in culture connect toform measurable networks on matrigel. This condition provides aphysiologically relevant environment for studying cell morphology,cellular biochemical functions, cell motility or invasions, and geneexpression. After one day these networks degenerate and edges retract toleave behind measurable aggregates.

Eight parameters are used to separate AD fibroblasts from age matchedcontrols (AC) and to non-Alzheimer's dementia (Non-ADD) at 48 hoursafter plating on matrigel:

1. Existence of large aggregates.

2. Attachment of cells to the aggregates.

3. Evidence of aggregates growing.

4. Small number of aggregates (<10 on a 10× image).

5. Large number of aggregates (>10 on a 10× image).

6. Measurable edges within networks.

7. Evidence of cell migrations.

8. Closeness to percolation limit (cells form continuous streams).

From these 8 parameters a quantitative score is introduced as follows:

1. The first tour parameters above are specific to Alzheimer's disease(AD) and score with “−1” for each if present and with “0” if absent.

2. The last four parameters are specific to non-AD and AC, and scorewith “+1” if present and with “0” if absent.

3. A total score is calculated as the sum of all eight values. If thetotal score is positive or zero the cells are AC or Non-ADD. If thetotal score is negative the cells are AD.

The total score representing the sum of eight characteristics of skincell fibroblasts at 48 hours after plating is represented in the FIG. 4.

Method 2—Area Per Number of Aggregates

Two of the eight parameters are expressed in the measure area per numberof aggregates, which is considerably higher for AD than for AC, andnon-ADD (Diagnostic accuracy 96%, N=31 (n_(AD)=12, n_(AC)=10, andn_(Non-ADD)=9) p<0.000001 for AD vs AC, and p<0.00001 for AD vsnon-ADD).

The AD cells show big, isolated aggregates, and little or no migrations(FIG. 5A). The normal controls and non-ADD fibroblasts show numeroussmaller clumps and high level of migration between the aggregates(Figure SB).

Method 3—Cell Migration

Unlike the Integrated Score Method, the Cell Migration Method is able todistinguish between AD, AC and non-ADD cells. See FIGS. 9 and 10.

Freely migrating cells are counted at 48 hours, N_(t), and approximately7 hours later, N2, and the migration rate is calculated asR=(N2−N_(t))/L\T, where L\T is the time interval between counts. Afreely migrating cell is a cell which is not attached to the aggregates,as depicted by the red dots in FIG. 8.

The population data (FIGS. 9, 10) shows that Alzheimer's diseasefibroblasts (AD-green squares) and non-Alzheimer's dementia fibroblasts(Non-ADD—blue triangles) have a significantly smaller number ofmigrating cells and rate of migration when compared with age matchedcontrol fibroblasts (AC red circles). Alzheimer's disease fibroblasts(green squares) show the smallest number of migrating cells and thelowest migration rate while age matched controls (red circles) show thehighest number of migrating cells and the highest migration rate.Interestingly non-ADD cells separate (with one exception) from AD and AC(FIGS. 5 and 6).

From the point of view of migration Non-Alzheimer's dementia fibroblastsseparate well from Alzheimer's disease fibroblast.

Method 4—Fractal Analysis

Unlike the Integrated Score Method, the Fractal Analysis Method is ableto distinguish between AD, AC and non-ADD cells (p<0.01). See FIG. 11B.

The fractal analysis method utilizes the complexity of the networks asmeasured by fractal dimension. Cells, preferably fibroblasts, taken frompatients suffering from Alzheimer's Disease have a statisticallysignificant lower fractal dimension than AC cells when grown in tissueculture. The complexity of the networks measured by this physicalparameter is also markedly different for fibroblasts taken from AD whencompared to AC and non-ADD fibroblasts. After network degeneration (˜48h), cells migrate and within a few days reach confluence. This recoveryis captured by a linear increase in fractal dimension (FIG. 11A). Theslope versus the intercept of each curve that tracks fractal dimensionas a function of time is markedly different in the three groups AC, AD,and Non-ADD (96% accuracy, n=3 1 (N_(AD)=12, N_(AC)=10, N_(non-ADD)=9);p<0.0001 for AD vs AC, and p<0.00001 for AD vs non-ADD). Unlike thefirst method the second one distinguishes between AC and non-ADD(p<0.01) (FIG. 11B).

Method 5—Lacunarity Analysis

The lacunarity analysis method quantifies the gaps of the fibroblastpatterns and is a complementary measure of complexity used as a secondlevel of discrimination. The average lacunarity of the fibroblasts isalso higher for fibroblasts taken from AD when compared to AC andnon-ADD fibroblasts. Typically, the lacunarity increases and peaks whenthe network degeneration is maximal i.e. when only isolated aggregatesare visible (FIG. 12A). The lacunary drops as the network regenerationstarts.

These measures of the dynamics of complexity, offer a new opportunity todiagnose AD patients with a minimally invasive procedure. The simplicityand low cost of the method are a useful screen for AD patients. Humanskin fibroblast networks like the neural networks in the AD brain show areduction in complexity as measured by fractal dimension. Human skinfibroblast networks provide a model of brain networks useful foraccurate AD diagnosis and drug screening.

Impaired Vertical Migration of Alzheimer's Disease Fibroblasts.

The same number of fibroblast cells (50 cells/mm) was plated onincreasing volumes of matrigel, from 400 μl to 800 μl with an incrementof 100 μl, on 12 well plates for an AD cell line. The increase in thematrigel volume, V, produces a proportional increase of the thickness ofthe matrigel layer, h, according to the relation: V=(nr2) h, where r=l1.05 mm (FIG. 13).

The vertical cell migration from the top surface to the bottom surfacebecomes more difficult with the increase in the thickness of thematrigel layer. This difficulty in migration is quantified here by thefractal dimension, lacunarity and number (FIG. 14).

After approximately 24 hours the networks degenerate and aggregates areleft behind. Here we show the dependence of the area per number on theinitial volume of matrigel (FIG. 12). For small volumes of matrigel,400, and 500 μl, there are no aggregates while for larger volumes, >500μl, the area of aggregates divided by their number is a curve whichpeaks at 700 μl. For a very limited number of the Alzheimer's diseasecases the area divided by number of aggregates is near the threshold(see FIG. 6) and a measure of aggregates at a later time will help tobetter separate these cases. After 79 h these aggregates increase insize and their number decreases so that the ratio area/number increaseseven further (green curve in FIG. 15A). For both 48 and 79 hours theeffect is optimum for an initial volume of 700 μl. The rate of changefor the area/number, FIG. 3B, is also a curve with a peak, enforcing theidea that at optimum initial volume of matrigel is 700 μl.

In the experiments presented above we used 1.5 ml Dulbecco's ModifiedEagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1%penicillin/streptomycin (PS). Serum starvation will have a further majorperturbation of the measures presented.

Fractal Dimension Methods

In one embodiment, the fractal dimension is calculated using a standardbox counting procedure after the raw images, which may be digitalimages, are filtered through an edge detection procedure which uses, forexample the difference of two Gaussians. AD can be diagnosed based onthe quantitative image analysis of cultured human skin fibroblasts. Inone embodiment, samples are taken through punch-biopsy. In general, asurgical blade can be used. The population data show that AC cases havea significantly higher fractal dimension than that of AD cases. Areduced complexity of human skin fibroblast networks AD cases providesdistinctions from AC and non-AD dementia cases.

Other image processing routines can be used with the invention insteadof box counting or line detection,

The simplicity and low cost of the method is helpful for screening ADpatients before resorting to other elaborate and costly techniques.Human skin fibroblast networks, like the neural networks in AD brain,show a reduction in complexity as measured by fractal dimension. In oneembodiment, human skin fibroblasts networks may be a model of brainnetworks that may be useful for new drug screening.

FIG. 16 depicts age matched control (AC) fibroblasts networks after 24hours of incubation. In one embodiment, a digital image of the networkis taken. FIG. 17 depicts Alzheimer's Disease (AD) patient fibroblastsnetworks after 24 hours of incubation. In one embodiment, a digitalimage of the network is taken. FIG. 18 depicts the fractal dimensions ofAC and AD subjects versus time. The dynamics of cellular networkmeasured by fractal dimension for the two cell lines shows a higherfractal dimension for AC than for AD. A significant separation isnoticeable after approximately a few hours of incubation. FIG. 19depicts a scatter plot the fractal dimension of AD versus AC networksafter 24 hours of incubation.

A fractal is generally a rough or fragmented geometric shape that can besplit into parts, each of which is (at least approximately) areduced-size copy of the whole, a property called “self-similarity.” Theobject (fractal) need not exhibit exactly the same structure at allscales, but the same “type” of structures must appear on all scales.Human skin fibroblast networks are an example of naturally-occurringfractals.

Consider a line. If the line is subdivided in half, it takes two ofthese halves to recreate the original line. If the line is subdividedinto four pieces, it takes four of them to cover the line. Generally,given a line segment of length “s,” the number of segments that willcover the original line is given by N(s)=(1/s)^(t).

Consider a square. If the square is subdivided into smaller squares,each with one half the side length then it takes four (2²=4) of thesesmaller squares to form the original square. If the square is subdividedinto smaller squares each with one quarter of the side length then ittakes sixteen (2⁴=16) of them to form the original square. As above wecan write an expression for the number of pieces we need of size “s” tocover the original square, it is N(s)=(1/s)2. Fora cube, the result isN(s)=(1/s)3.

The exponents 1, 2, and 3 in the above examples are the dimensions ofthe line, square, and cube respectively. This can be generalized toN(s)=(1/s)° here Dis the dimension, an integer as above, but it need notbe. If we take logarithms of both sides, we have log(N(s))=D log(1/s),in order words we can estimate the dimension by plotting log(N(s))against log(1/s) the slope (D) of which is the dimension. If the slopeis a non-integer, then the object is a fractal, and the dimension is afractional (fractal) dimension.

Complexity is the study of how living and nonliving things organizethemselves into patterns and interact as systems. Complexity isextremely multidisciplinary and involves scientists in a vast assortmentof fields from biology to physics. Complexity of human skin fibroblastnetworks can be quantified by computing their fractal dimensions.

In one embodiment, edge detection is used in the present invention. Edgedetection is a term used in the field of image processing, particularlyin the areas of feature detection and feature extraction, to refer toalgorithms which aim at identifying points in a digital image at which,for example, the image brightness changes sharply or has otherdiscontinuities.

It can be shown that under rather general assumptions for an imageformation model, discontinuities in image brightness are likely tocorrespond to one or more of discontinuities in depth, discontinuitiesin surface orientation, changes in material properties and variations inscene illumination.

In the ideal case, the result of applying an edge detector to an imagemay lead to a set of connected curves that indicate the boundaries ofobjects, the boundaries of surface markings as well curves thatcorrespond to discontinuities in surface orientation. Thus, applying anedge detector to an image may significantly reduce the amount of data tobe processed and may therefore filter out information that may beregarded as less relevant, while preserving the important structuralproperties of an image. If the edge detection step is successful, thesubsequent task of interpreting the information content in the originalimage may therefore be substantially simplified.

There are many methods for edge detection, but most of them can begrouped into two categories, search-based and zero-crossing based. Thesearch-based methods detect edges by first computing a measure of edgestrength, usually a first-order derivative expression such as thegradient magnitude, and then searching for local directional maxima ofthe gradient magnitude using a computed estimate of the localorientation of the edge, usually the gradient direction. Thezero-crossing based methods search for zero crossings in a second-orderderivative expression computed from the image in order to find edges,usually the zero-crossings of the Laplacian or the zero-crossings of anonlinear differential expression. As a pre-processing step to edgedetection, a smoothing stage, for example Gaussian smoothing, may beapplied. In other embodiments noise filtering algorithms may beemployed.

The edge detection methods that have been published mainly differ in thetypes of smoothing filters that are applied and the way the measures ofedge strength are computed. As many edge detection methods rely on thecomputation of image gradients, they also differ in the types of filtersused for computing gradient estimates in the x- and y-directions.

In one embodiment, the method uses a box counting procedure. The imageis covered with boxes, for example by a computer. The goal is to findhow the number of boxes needed to cover the image changes with the sizeof the boxes. If the object is I-dimensional, such as a line, we expectN(s)=(Vs)¹, as described above. And so on for higher dimensions. Such aprocedure can be implemented on a computer using the digital images ofthe samples.

In one embodiment a database can be made of many differentnon-Alzheimer's control (AC) subjects of various ages. The database canbe made such that the human subject being tested can be evaluated versusage-matched AC data.

In one embodiment, the complexity of the fibroblast networks 1squantified by measurement of fractal dimension and lacunarity curves.The complexity of the networks measured by these physical parametersalso markedly differs for fibroblasts taken from AD when compared to ACand non-ADD fibroblasts. After network degeneration, by way of exampleafter approximately 48 hours, cells migrate and within a few days reachconfluence. In one embodiment, this recovery is captured by a linearincrease in fractal dimension. The slope versus the intercept of eachcurve that tracks fractal dimension as a function of time is markedlydifferent in the three groups AC, AD, and non-ADD (100% accuracy, n=26(AD=10, AC=10, non-ADD=6); p<0.0001 for AD vs AC, and p<0.00001 for ADvs non-ADD). This method shows distinguishable differences between ACand non-ADD (p<0.01).

Methods Utilizing Cell Morphology Characteristics

Within a short time after being cultured, for example within an hour,measurable networks form. In one embodiment, culturing takes place in agelatinous protein mixture which provides a viable environment forstudying cell morphology. After a time, for example after about one day,these networks degenerate and edges retract to leave behind measurable“clumps” or aggregates.

As with any of the methods of the invention, the image may be preparedby obtaining a cell or a sample and culturing or incubating the cell orsample for a period of time. In one embodiment, the period of time isabout 48 hours or any one-hour increment subdivision thereof. During theperiod of time, the cell or sample fibroblast network changes. An imageis then taken. Quantitative, qualitative, and semi-quantitativeinformation can be gathered from the image.

(4) In one embodiment, certain characteristics of the image can beassigned values. For example, by inspecting the image, the followingnon-exhaustive, and non-limiting characteristics can be ascertained andoptionally assigned values: (1) Are there big clumps? (2) Are the cellsattached to the clumps? (3) Are the big clumps growing? (4) Are therejust a few clumps? For example, less than or equal to five on a 10×image? (5) Are there multiple clumps (for example, greater than five ona 10× image)? (6) Are there remnant edges from a network previouslyformed (for example, in matrigel)? (7) Are there many cells migrating?(8) Are the cells near percolation (i.e., cells which form asubstantially continuous stream from left right or up down of theimage)?

In some embodiments, only a partial listing of these characteristics maybe considered. Two of the eight parameters are expressed in the ratio ofa measured area per number of aggregates. This ratio is considerablyhigher for AD than for age matched controls (AC), and non-Alzheimer'sdegeneration (non-ADD) (Diagnostic accuracy 96%, N=30 (AD=12, AC=10, andnon-ADD=8) p<0.000001 for AD vs AC, and p<0.00001 for AD vs non-ADD).Any or even all of these characteristics can be ascertained manually orvia image processing methods as is known in the relevant arts.

In one embodiment, the “characteristics,” for example the eightcharacteristics (or a subset thereof or an augmented set ofcharacteristics) are assigned values. The values can be assignedaccording to correlation studies, for example according to beingcorrelated with AD cells or being correlated with AC or non-ADD cells.In one embodiment, the characteristics (1) through (4) mentioned aboveare correlated with AD fibroblasts, and are then assigned a value of,for example −1 if present or O if absent. The actual values are given byway of example only, as other values can also be assigned. In oneembodiment, characteristics (5) through (8) mentioned above arecorrelated with AC and non-ADD fibroblasts. Parkinson's Disease (PD) andHuntington's Disease (HD) are non-limiting examples of non-ADD cells.Characteristics (5) through (8) are assigned a value of +1 if present orO if absent. In one embodiment, the assigned values can be summed foreach clump. The summed values can then be plotted, as is shown in FIG.4.

In another embodiment, the values of the characteristics can be assignedintermediate values according to the “strength” of the characteristicbeing measured. For example, the characteristic (1) “are there bigclumps” ? can be assigned any intermediate value between −1 (forextremely large clumps) through zero (for extremely small clumps). Forexample, a value of −0.9 can be assigned for relatively “large” clumps,a value of −0.8 assigned to slightly smaller (yet still “large”) clumps,and so on. A graduated scale for any of the above-mentionedcharacteristics (or others) can be formulated through routineexperimentation. In one embodiment, the method can be fully automatedusing image processing techniques, and moreover all (or perhaps onlysome) of the characteristics can be quantified on a fully graduated,i.e., digital, basis.

As illustrated in FIG. 4, AD cells, such as those shown in FIG. SAcharacteristically display big, isolated clumps with little to nomigration compared to AC cells and non-ADD cells. Consequently, the ADcells typically have values summing to relatively low numbers, typicallynegative numbers, in this scheme. The normal controls and non-ADDfibroblasts, such as those shown in Figure SB show numerous smallerclumps and high level of migration between the clumps. Consequently, theAC and non-ADD cells typically have values summing to relatively highnumbers, typically positive numbers, in this scheme. The above methodprovides yet another way for diagnosing AD.

Methods Utilizing Area

In another embodiment, the area of clumps is calculated. For example,the area of the clumps shown in Figure SB (AC cells) is calculated. Thiscan be done by any suitable method, for example but not limited to, byfitting an ellipse across the clump. The clumps can then be com1ted onthe images. The counting as well as area calculation can either be donemanually or can be automated, for example by image processing techniquesknown in the relevant arts. The numbers shown on Figure SB represent thearea of the clumps in square microns, μ² Similarly, the area of ADcells, such as those shown in Figure SA, can be calculated. By way ofexample, the area shown on Figure SA is 12,670 μ2, a much larger areathan associated with the areas of the AC cells depicted in FIG. 5B. Thearea per number of clumps can be plotted as is depicted in FIG. 7.

FIG. 7 is a logarithmic plot of the area per number of clumps ascalculated by the above method. Of note, the area per number of clumpsfor AD cells is significantly higher than the area per number of clumpsfor either the AC or the non-ADD cells. The above method provides yetanother way for diagnosing AD.

In other embodiments of the invention, any of the above methods can becombined. For example, the fractal dimension can be calculated, and/orthe characteristics can be assigned and summed, and/or the area pernumber of clumps can be calculated. In one embodiment, a positivediagnosis for AD is made only when two or more of the above methodsindependently would indicate a positive diagnosis. In other embodiments,a positive diagnosis for AD is made only when all methods (for examplethree different methods, specifically for example, the fractaldimension, summation of characteristics, and area methods) wouldindependently indicate a positive diagnosis. In other embodiments, falsepositives and negatives can be avoided or minimized by adjusting thedefinition of “statistically significant,” for example by setting adiagnosis threshold at a certain multiple of population standarddeviations for any of the above-mentioned variables.

In any embodiments of the invention, a cell may be cultured or incubatedin a protein mixture. In one embodiment, the protein mixture is agelatinous protein mixture. A non-limiting exemplary gelatinous proteinmixture is Matrigel™. Matrigel™ is the trade name for a gelatinousprotein mixture secreted by Engelbreth-Holm-Swarm (EHS) mouse sarcomacells and marketed by BD Biosciences. This mixture resembles the complexextracellular environment found in many tissues and is used by cellbiologists as a substrate for cell culture. BD Bioscience maintains awebsite at http://www.hdbiosiences.ca.

In one embodiment, a cell is cultured or incubated in a basementmembrane preparation. In one embodiment, this preparation issolubilized. In one embodiment, a basement membrane preparation isextracted from a tumor. In one embodiment, the tumor is theEngelbreth-Holm-Swarm (EIS) mouse sarcoma, a tumor rich in extracellularmatrix proteins. Its major component is laminin, followed by collagenIV, heparan sulfate proteoglycans, entactin/nidogen. In certainembodiments, this preparation contains TGF-beta, epidermal growthfactor, insulin-like growth factor, fibroblast growth factor, tissueplasminogen activator, and/or other growth factors which may or may notoccur naturally in the EHS tumor.

In one embodiment, a cell is cultured or incubated in a preparationcomprising extracellular matrix proteins. In one embodiment, thepreparation comprises laminin, collagen, heparin sulfate proteoglycans,entactin/nidogen, and/or combinations thereof. In one embodiment, thepreparation is extracted from a tumor. In one embodiment, the tumor isthe Engelbreth-Holm-Swarm (EHS mouse sarcoma. In one embodiment, thepreparation further comprises growth factor. In one embodiment, thepreparation further comprises TGF-beta, epidermal growth factor,insulin-like growth factor, fibroblast growth factor, tissue plasminogenactivator, and/or combinations thereof, and/or other growth factors. Inone embodiment, the TGF-beta, epidermal growth factor, insulin-likegrowth factor, fibroblast growth factor, tissue plasminogen activator,and/or other growth factors occur naturally in a tumor. In oneembodiment, the growth factors occur naturally in the EHS mouse sarcoma.

In one embodiment, the preparation comprises an extracellular matrixprotein preparation which is effective for the attachment anddifferentiation of both normal and transformed anchorage dependentepithelioid and other cell types. These include neurons, hepatocytes,Sertoli cells, chick lens, and vascular endothelial cells. In oneembodiment, the extracellular matrix protein preparation may influencegene expression in adult rat hepatocytes as well as three-dimensionalculture in mouse and human mammary epithelial cells. In one embodiment,this is the basis for several types of tumor cell invasion assays, willsupport in vivo peripheral nerve regeneration, and provides thesubstrate necessary for the study of angiogenesis both in vivo and invivo. In one embodiment, an extracellular matrix protein also supportsin tit propagation of human tumors in immunosuppressed mice.

In one embodiment, a volume of chilled extracellular matrix protein isdispensed onto tissue culture labware. As used herein, “chilled” refersto a temperature less than room temperature, preferably less than about15° C., more preferably less than about 10° C., more preferably lessthan about 5° C., most preferably about 4° C. When incubated at anelevated temperature, the extracellular matrix proteins self-assembleproducing a thin film that covers the surface of the labware. As usedherein, “elevated” refers to a temperature above room temperature,preferably above about 20° C., more preferably above about 25° C., morepreferably above about 30° C., more preferably above about 35° C., andmost preferably about 37° C., which is approximately average human bodytemperature.

Cells cultured on extracellular matrix protein demonstrate complexcellular behavior that is otherwise difficult to observe underlaboratory conditions. For example, endothelial cells create intricatespider web-like networks on extracellular matrix protein coated surfacesbut not on plastic surfaces. Such networks are highly suggestive of themicrovascular capillary systems that suffuse living tissues with blood.Hence, the process by which endothelial cells construct such networks isof great interest to biological researchers and extracellular matrixproteins allow them to observe this.

In some embodiments, it may be preferable to use greater volumes ofextracellular matrix proteins to produce thick three-dimensional gels.The utility of thick gels is that they induce cells to migrate from thesurface to the interior of the gel. In some embodiments, this migratorybehavior is studied by researchers as a model of tumor cell metastasis.

The ability of extracellular matrix proteins to stimulate complex cellbehavior is a consequence of their heterogeneous composition. In someembodiments, the chief components of extracellular matrix proteins arestructural proteins such as laminin and collagen which present culturedcells with the adhesive peptide sequences that they would encounter intheir natural environment. Some embodiments also employ growth factorsthat promote differentiation and proliferation of many cell types.Extracellular matrix proteins may also contain numerous other proteinsin small amounts.

Measures of the dynamics of fibroblast network complexity, as disclosedherein, offer a new opportunity to diagnose AD patients with a minimallyinvasive procedure. Human skin fibroblast networks, like the neuralnetworks in the AD brain, show a reduction in complexity as measured byfractal dimension compared to AC and non-ADD cells. Human skinfibroblast networks provide a model of brain networks useful foraccurate AD diagnosis and drug screening.

All books, articles, or patents references herein are incorporated byreference to the extent not inconsistent with the present disclosure.The present invention will now be described by way of examples, whichare meant to illustrate, but not limit, the scope of the invention.

Example 1: Coating the 12 Well Plates with BD Matrigel Matrix GrowthFactor Reduced

Equipment and Materials: Class II A/B 3 biological safety cabinet (FormaScientific). CO2 water-jacket incubator (Forma Scientific). Invertedmicroscope. Pasteur pipettes. Serological pipettes. Pipette aids (OmegaCat. No. P5017). BD Matrigel Matrix Growth Factor Reduced (BDBiosciences, Cat. No. 354230), (Aliquot 800 μl and store at −20° C.).Sterile 12 well culture plates (Coming Inc., Cat. No. 3512)

Procedure: Thaw BD Matrigel Matrix Growth Factor Reduced at 4° C. on ice30 min. before use, and use pre-cooled pipettes, tips, and 12 wellculture plates. Make sure Matrigel is liquid and has no solidaggregates.

Thick Gel Method: Using cooled pipettes, mix the BD Matrigel MatrixGrowth Factor Reduced to homogeneity. Keep 12 well culture plates on ice30 min. prior to use and during the adding of BD Matrigel Matrix GrowthFactor Reduced, 700 μL per well. Verify the homogeneity of the gel onthe surface of the cell culture plates under the inverted microscope,and avoid bubbles. Place 12 well plates at 37° C. for 30 minutes. Addthe cell suspension on top of BD Matrigel Matrix Growth Factor Reduced.The density of cells is adjusted to 50 cells/mm (See below).

Example 2: Preparing of Human Skin Fibroblast for Plating

Equipment and Materials: Class II A/B 3 biological safety cabinet (FormaScientific). CO2 water-jacket incubator (Forma Scientific). Invertedmicroscope. T-E (Trypsin-EDT A solution 1×) (stored at ˜20 C). M-2(Medium-2) DMEM with 10% FBS, and 1% PS. Pasteur pipettes. Serologicalpipettes. Pipette aids (Omega Cat. No. P5017). Culture flask, vent cap,25 cm². 15 ml and 50 ml sterile plastic tube. 500 ml Bottle Top Filter.Water bath Centrifuge.

Procedure: Thaw and warm T-E and M-2 medium at 37° C. in the water bath.

Flask cultures containing tissue fragments: Remove and discard culturemedium from flask by suction. To eliminate serum residue that couldinactivate trypsin, add 2 ml T-E and suck out immediately. Add 2 ml ofT-E to flask and incubate at 37° C. for 3-5 minutes. Time of detachmentof cells from the surface of culture flasks is not the same for allpatients and needs to be adjusted for each case in the range 3-5minutes. Observe the cells under microscope: if rounded, they aredetached. If most are not rounded, leave the suspension in the incubatorfor another minute or two until they appear rounded. Add 5 ml of M-2medium to inhibit trypsin activity. Gently triturate by pipetting todetach cells from the bottom of the flask, but be careful not to touch,or detach, the tissue fragments. Transfer the cells suspension (bypipette) to a 15 ml sterile plastic tube, centrifuge it at 1000 RPM(speed 3) for 5 minutes, discard the supernatant, and suspend the cellsin 3 ml M-2 medium. Gently triturate by pipetting to detach cells fromthe bottom of the 15 ml sterile plastic tube.

Example 3: Counting of Human Skin Fibroblasts

Equipment and Materials: Class II A/B 3 biological safety cabinet (FormaScientific). Inverted microscope. Cell counting chamber-Ley Double (VWRscientific, Cat. No. 15170-208). Pasteur pipettes. Serological pipettes.Pipette aids (Omega Cat. No. P5017). Sterile 12 well culture plates(Coming Inc., Cat. No. 3512)

Procedure: Add 0.25 ml of cell suspension into the cell counting chamberand put the cover glass on the top.

Cell counting chamber-Levy Double containing fibroblast cells: Let thecell stabilize and then count the number of cells in the nine bigsquares under the inverted microscope. The average number of cells(AvC), multiplied by 10, gives the density of cells (DC) expressed innumber of cells/mm³. Dilute the cell suspension with M-2 medium to reachthe density of 50 cells/mm³ in a total volume of 1.5 ml. Use (1.5ml)×(50)/AvC for the cell suspension and complete the rest up to 1.5 mlwith M-2 medium. Three wells are used for each cell line. Therefore,multiply the numbers in step 3 by 3. Prepare the 4.5 ml mixture in a 15ml sterile plastic tube and gently homogenize using a 10 ml pipettes.Add 1.5 ml in each of the three wells. Label the three well plates withpatient code, date, and passage number. Spray outside of 12 well cultureplates with 70% EtOH and place in the incubator.

Example 4: Verifying the Initial Cell Density of Human Skin FibroblastThrough Image Analysis

Equipment and Materials: Inverted Microscope. Image J.

Procedure: After 10 minutes in the incubator take the 12 well cultureplate out and put it under the inverted microscope.

Cell counting using image analysis: Under the 4× objective align thecenter of the well with the center of the viewing field. Change theobjective to 10× and take one image in the center plus other four bymoving one field of view to the left/right, and up/down. Load the imageunder ImageJ and go to Process/Noise/Despeckle. Then go toProcess/Noise/Binary/MakeBinary. Despeckle the binary image 2-3 timesthen use Analyze/Analyze Particles for counting the cells. The result isunder Summary/Count. Be aware that automatic counting of cellsoverestimates the manual counting by ˜12%. The lower threshold forinitial cell density is 45 cell/mm³, which corresponds to a cell numberof 190 cells under 10×, and to a fractal dimension of 1.4. The higherthreshold for initial cell density is 62 cell/mm³, which corresponds toa cell number of 650 cells under 10×, and to a fractal dimension of1.62. Any well that has an average number of cells outside the twothresholds is discarded.

Example 5: Method 1; Scores

Equipment and Materials: Inverted microscope (Westover Digital AMIDModel 2000). Micron 2.0.0 Westover Scientific 2008. Image J

Procedure: Pictures taken at 48 hours and after to measure total scorebased on 8 criteria. Three criteria (1, 4, and 5 see below) arerepresented quantitatively by the average area per number of aggregates.

Parameters used for screening:

-   -   1. Existence of large aggregates.    -   2. Attachment of cells to the aggregates.    -   3. Evidence of aggregates growing.    -   4. Small number of aggregates (<10 on a 10× image).    -   5. Large number of aggregates (>10 on a 10× image).    -   6. Measurable edges within networks.    -   7. Evidence of cell migration.    -   8. Closeness to percolation limit (cells form continuous        streams).

Total score: (1) First four parameters are specific to Alzheimer'sdisease (AD) and score with “−1” if present and with “0” if absent. (2)The last four parameters are specific to age matched controls (AC) andto non Alzheimer's dementias (Non-ADD), and score with “+1” if presentand with “0” if absent. (3) Calculate the total score as the sum of alleight values. If total score is positive or zero the cells is AC orNon-ADD. If total score is negative the cells are AD.

Average area per average number of aggregates: (1) Import images intoMicron 2.0.0 and under Measurement/Ellipse Area measure the aggregatesone by one. Fit an ellipse on aggregate and area is providedautomatically by the software. (2) Collect the areas in a spreadsheetand extract the number of aggregates automatically with the functionCOUNT. (3) Calculate the average area and the average number ofaggregates for each image as well as the ratio of the two. (4) Averagethe area per # aggregates for all five images for each well. (5) Averagethe area per # aggregates for all three wells for the same cell line.(6) If area per # aggregates is smaller than 1000 the cell lines are ACor Non-ADD and if it is bigger than 1000 then the cells are AD.

Example 6: Method 2; Fractal Analysis

Equipment and Materials: Inverted microscope (Westover Digital AMIDModel 2000). Image J. Plug in FracLac.

Procedure: Pictures taken after 48 hours and calculate fractaldimension.

Parameters used for screening: (1) Existence of large aggregates.

Example 7: Preparation of Mediums

Preparation of mediums: DMEM (high glucose), Cat. No. 10313-039,Invitrogen Gibco (Store in 4° C. refrigerator); FBS, Cat. No. 10082-147,Invitrogen Gibco (Aliquot 50 ml and store at −20° C.); PS (Penicillinand streptomycin solution) Cat. No. 15140-122, Invitrogen (Aliquot 5 mland store at −20° C.). M-1 (Medium-1) DMEM with 45% and 1% PS. M-2(Medium-2) DMEM with 10% and 1% PS. Filter, label and store in 4° C.refrigerator, up to 1 month).

1.-94. (canceled)
 95. A composition of matter comprising (i) 700 μl ofBD Matrigel Matrix Growth Factor Reduced having on top of it (ii) asuspension of human skin fibroblasts.
 96. The composition of claim 95,wherein the Matrigel Matrix Growth Factor Reduced is homogeneous. 97.The composition of claim 95, wherein the Matrigel Matrix Growth FactorReduced is at a temperature of 37° C.
 98. The composition of claim 95,wherein the suspension of human skin fibroblasts is at a density havinga lower threshold of 45 cells/mm³ and a higher threshold of 62cells/mm³.
 99. The composition of claim 95, wherein the suspension ofhuman skin fibroblasts is at a density of 50 cells/mm³.
 100. Thecomposition of claim 95, wherein the composition of matter is present ina well within a 12-well culture plate.
 101. A composition of mattercomprising (i) 700 μl of BD Matrigel Matrix Growth Factor Reduced havingon top of it (ii) a suspension of human skin fibroblasts, wherein (i)the Matrigel Matrix Growth Factor Reduced is homogeneous, (ii) theMatrigel Matrix Growth Factor Reduced is at a temperature of 37° C.,(iii) the suspension of human skin fibroblasts is at a density of 50cells/mm³, and (iv) the composition of matter is present in a wellwithin a 12-well culture plate.
 102. A method for making a compositionof matter comprising (i) 700 μl of BD Matrigel Matrix Growth FactorReduced having thereupon (ii) a suspension of human skin fibroblasts,which method comprises the step of placing a suspension of human skinfibroblasts on top of 700 μl of BD Matrigel Matrix Growth FactorReduced.
 103. The method of claim 102, wherein the Matrigel MatrixGrowth Factor Reduced is homogeneous.
 104. The method of claim 102,wherein the Matrigel Matrix Growth Factor Reduced is at a temperature of37° C.
 105. The method of claim 102, wherein the suspension of humanskin fibroblasts, once atop the Matrigel Matrix Growth Factor Reduced,is adjusted to a density having a lower threshold of 45 cells/mm³ and ahigher threshold of 62 cells/mm³.
 106. The method of claim 102, whereinthe suspension of human skin fibroblasts, once atop the Matrigel MatrixGrowth Factor Reduced, is adjusted to a density of 50 cells/mm³. 107.The method of claim 102, wherein the composition of matter is present ina well within a 12-well culture plate.
 108. A method for making acomposition of matter comprising (i) 700 μl of BD Matrigel Matrix GrowthFactor Reduced having thereupon (ii) a suspension of human skinfibroblasts, which method comprises the step of placing a suspension ofhuman skin fibroblasts on top of 700 μl of BD Matrigel Matrix GrowthFactor Reduced, wherein (i) the Matrigel Matrix Growth Factor Reduced ishomogeneous, (ii) the Matrigel Matrix Growth Factor Reduced is at atemperature of 37° C., (iii) the suspension of human skin fibroblasts,once atop the Matrigel Matrix Growth Factor Reduced, is adjusted to adensity of 50 cells/mm³, and (iv) the composition of matter is presentin a well within a 12-well culture plate.